I can see why they wouldn't want to help too much in offensive situations (I think the logic is that they won't come to help you attack unless your force is at least twice the power of the AIs). However, there's also the irony of, if your force is twice the size of theirs, why would you need help?
On defense I can also see the self-preservation bit coming into play. Still, it's odd that if Enclaves are so concerned about self-preservation, they'll still run through enemy-controlled planets to get to their destination when they could pass through allied planets to get there as well.
Either way, I think the Enclave changes are fantastic and I've still got a lot of experimenting to do with them before I come to any reasonable conclusion about it.
Assuming that Roaming Enclaves are supposed to be as much of a threat as they are a boon, my initial impression is that the allied Enclaves are much smarter, and therefore last much longer than the enemy Enclaves, which pretty much just spawn and die within a few seconds. Therefore, the player gets a huge surplus of powerful allied Enclaves, which ironically can be used to defend against the enemy Enclaves, eventually making the "threat" portion of the Roaming Enclaves Faction a non-issue.
I could see several ways of addressing this, but like I said, there's still testing to be done. Despite these minor flaws, I still love it.